Sodium in PDB 3si4: Human Thrombin in Complex with UBTHR104

All present enzymatic activity of Human Thrombin in Complex with UBTHR104:
3.4.21.5;

The structure of Human Thrombin in Complex with UBTHR104, PDB code: 3si4 was solved by A.Biela, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.60 / 1.27
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.350, 71.230, 72.590, 90.00, 100.36, 90.00
R / Rfree (%)	13.7 / 15.9

The binding sites of Sodium atom in the Human Thrombin in Complex with UBTHR104 (pdb code 3si4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Thrombin in Complex with UBTHR104, PDB code: 3si4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Thrombin in Complex with UBTHR104


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Thrombin in Complex with UBTHR104 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na4 b:12.8 occ:1.00 O H:THR172 2.3 12.5 1.0 O H:LYS169 2.4 13.2 1.0 O H:HOH1199 2.4 15.0 1.0 O H:HOH1233 2.5 18.9 1.0 O H:HOH1226 3.0 25.4 1.0 C H:LYS169 3.5 12.5 1.0 C H:THR172 3.6 12.8 1.0 CA H:ASP170 4.0 12.6 1.0 N H:ASP170 4.2 12.3 1.0 N H:THR172 4.3 12.8 1.0 CG H:LYS169 4.3 19.0 1.0 C H:ASP170 4.4 12.8 1.0 CA H:ARG173 4.4 13.3 1.0 N H:ARG173 4.4 12.2 1.0 O H:HOH1378 4.5 34.9 1.0 NZ H:LYS169 4.5 28.1 1.0 CA H:THR172 4.5 13.2 1.0 CA H:LYS169 4.5 12.2 1.0 OD1 H:ASP170 4.7 17.5 1.0 O H:ASP170 4.8 13.7 1.0 N H:SER171 4.8 12.6 1.0 CG2 H:THR172 4.9 14.7 1.0 CB H:LYS169 4.9 15.0 1.0 C H:ARG173 5.0 13.0 1.0

Sodium binding site 2 out of 2 in the Human Thrombin in Complex with UBTHR104


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Thrombin in Complex with UBTHR104 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na5 b:15.4 occ:1.00 O H:ARG221A 2.3 16.1 1.0 O H:HOH1239 2.4 16.1 1.0 O H:LYS224 2.4 13.6 1.0 O H:HOH1160 2.4 16.0 1.0 O H:HOH1055 2.5 13.9 1.0 O H:HOH1154 2.6 17.9 1.0 C H:ARG221A 3.4 16.1 1.0 C H:LYS224 3.4 13.0 1.0 N H:LYS224 3.8 15.4 1.0 N H:ARG221A 3.9 16.3 1.0 O H:HOH1050 3.9 14.0 1.0 O H:HOH1215 4.0 20.3 1.0 C H:ASP221 4.0 17.4 1.0 CA H:LYS224 4.1 14.2 1.0 O H:TYR184A 4.1 15.8 1.0 N H:ASP222 4.2 18.2 1.0 N H:GLY223 4.3 17.8 1.0 CA H:ARG221A 4.3 16.8 1.0 O H:HOH1114 4.3 14.1 1.0 CA H:ASP222 4.3 19.2 1.0 CA H:ASP221 4.4 17.2 1.0 N H:TYR225 4.4 11.8 1.0 CB H:LYS224 4.5 15.9 1.0 O H:ASP221 4.5 18.4 1.0 C H:ASP222 4.5 18.5 1.0 OD1 H:ASP221 4.6 17.2 1.0 CA H:TYR225 4.7 11.6 1.0 O H:HOH1218 4.8 18.3 1.0 C H:GLY223 4.9 15.9 1.0

A.Biela, M.Khayat, H.Tan, J.Kong, A.Heine, D.Hangauer, G.Klebe. Impact of Ligand and Protein Desolvation on Ligand Binding to the S1 Pocket of Thrombin J.Mol.Biol. V. 418 350 2012.
ISSN: ISSN 0022-2836
PubMed: 22366545
DOI: 10.1016/J.JMB.2012.01.054